A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery

Wednesday, February 07, 2007

Killer Co-evolution

To close up, for now, the story I've been spinning about cancer stroma from Day 1 & Day 2 of the Week of Science, I'll address a question which may have been prompted by yesterday's item about the symbiotic relationship between tumor and cancer stroma: How does this arise? What drives the stroma into being Benedict Arnold, and what chance is there to bring it back?

At the end of last year a paper came out in PNAS that looks at this question in a clever way. A challenge for studying cancer's interaction with its surrounding cellular environment is that it is very difficult to separate the two. How can you ever be sure you are looking at pure tumor or pure stroma?

The paper solves this problem by having the tumor come from one species and the stroma from another. Mouse xenograft models were built by injecting human tumor cell lines into immunodeficient mice. After tumors formed, the tumors were excised and then disaggregated into individual cells, and these cells sorted by flow cytometry. The tumor cells have higher DNA content than the mouse cells, so a DNA stain can sort one from the other. DNA from the mouse cells was then subjected to copy number analysis.

Copy number analysis is quite the rage these days, both for oncology and for looking at normal variation in the human genome. Most papers use array comparative genomic hybridization, or array CGH, to analyze copy number variation. This paper uses the closely related method ROMA, which differs in some key details but at a very high level is very similar. In short, the fragments from the genome are probed against a microarray which has markers spaced across each chromosome; by measuring the signals (and applying a lot of corrections, still being worked out), one can infer copy number changes ranging from complete losses of chromosome pieces to extreme amplifications.

ROMA provides another layer of filtration of the human tumor cells from mouse stromal cells, as the array probes shouldn't hybridize well cross-species. Normal tissue samples from the mice were used to normalize any murine copy number polymorphisms.

From seven tumors a number of genomic alterations were observed. This reinforces previous suggestions that the tumor stroma is co-evolving with the tumor, and that these changes are permanent since the genome itself is being altered. Two genes were observed to change copy number in models built from different tumor lines, while some other genes repeated in tumors built from the same line. However, no gene was universally observed to change copy number with the same cell line, suggesting that there are multiple co-evolutionary paths for successful tumor stroma.

This paper is just an crack into the field. In particular, they did not try to correlate their results with human clinical samples. The sample size here is very small, with only a few types of tumor lines tried. The functional roles of the altered genes was not explored. It is virtually a certainty (though I have no inside info) that such studies are ongoing -- especially since the lab involved has done all three of these in other papers. Of particular interest will be to better understand the mechanism of cancer stromal cell derangement. Is it purely an evolutionary selection for living near a tumor, or is the tumor somehow actively participating in the derangement by triggering mutagenic mechanisms or providing key survival signals?

A normal role for fibroblasts is to repair wounds, and hence the formation of tumor stroma may represent a repair attempt by the body which is co-opted by the tumor. Previous gene expression studies have identified a 'wound response signature' which is correlated with clinical outcome. Interestingly, the two genes reported to be the drivers of this signature did not show up in the ROMA analysis. This also suggests another line of experiment: do these mouse stromal cells exhibit the clinical signature?

Evolution, ecology & medicine all woven together -- it would be purely fascinating, if it weren't so deadly serious.

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About Me

Dr. Robison spent 10 years at Millennium Pharmaceuticals working with various genomics & proteomics technologies & working on multiple teams attempting to apply these throughout the drug discovery process. He spent 2 years at Codon Devices working on a variety of protein & metabolic engineering projects as well as monitoring a high-throughput gene synthesis facility. After a brief bit of consulting, he rejoined the cancer drug discovery field at Infinity Pharmaceuticals in May 2009. In September 2011 he joined Warp Drive Bio, a startup applying genomics to natural product drug discovery. Other recurring characters in this blog are his loyal Shih Tzu Amanda and his teenaged son alias TNG (The Next Generation).
Dr. Robison can be reached via his Gmail account, keith.e.robison@gmail.com
You can also follow him on Twitter as @OmicsOmicsBlog.